The next time Scotland face South Africa will be in Newcastle at next year’s World Cup and their head coach, Vern Cotter, whose first three matches in charge this month resulted in victories over the United States, Canada and Argentina, has little time to mould perennial also-rans in the Six Nations into a unit capable of toppling the second-ranked team in the world.

If Scotland were below strength in Port Elizabeth, so were the Springboks who had five uncapped players in their match-day 23 and were on the rebound after a fortuitous victory over Wales in Nelspruit the previous week. The match was all but over in the first 16 minutes after South Africa, moving the ball quickly from set-pieces and rucks, crafted three tries.

The Springboks lost their way after their influential scrum-half Fourie du Preez left the field with an ankle injury, but they rediscovered their verve after the break to establish a record score against Scotland at home. Cotter’s team, which included only three players who started the final match in the Six Nations against Wales, were overpowered and struggled to make use of the possession they secured, but they never capitulated.

“As much as we hate losing, especially by a score like that, there are some very positive things to come out of the defeat,” said Cotter. “All the players have done well on the tour but what this illustrated is that there are a number of things we have to go away and work on to become competitive before the World Cup.

“We have to keep doing the good things and take away the bad stuff. If we don’t offer as many opportunities to the opposition as we did on Saturday then we can shift in the right direction. It was a brave effort, the guys never gave up, but now it is a question of channelling energy and decision making in the right way.”

South Africa have not lost to anyone other than New Zealand in the past 21 months and under their head coach, Heyneke Meyer, they have become more fluid while remaining physical and direct. Their strength in depth masked chronic injury problems in the midfield and the second row, but they will be judged on how they fare against New Zealand in the Rugby Championship.

“I am very proud of the guys,” said Meyer. “The message was that we had to come back and make the country and team proud after the close call last week and we did that. One thing that stands out for me was us not conceding tries. We kept the Scots out for those last minutes when other teams would have leaked a try.”

Handre Pollard, the South Africa Under-20 captain, had a composed debut at fly-half, more of a running threat than Morne Steyn and a confident passer off either hand, while the second-row Lood de Jager scored the final two tries of the match. “We have 30 players out and it was good to see guys like Lood and Handre come through,” said Meyer.

“First-choice players are coming under pressure and a number of the merging players will be contenders for places in the squad for the Rugby Championship. Once everyone is fit, we will have difficult choices to make.”

Cotter will not have as many options as he ponders an autumn campaign that includes an encounter with New Zealand. “It was a tough tour playing in four different countries, but there is a lot we can take from it,” said the prop Alasdair Dickinson. “A number of young players have won their first cap and it is onwards and upwards from now.”